Package: methylInheritance 1.37.0

Astrid Deschênes

methylInheritance: Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.

Authors:Astrid Deschênes [cre, aut], Pascal Belleau [aut], Arnaud Droit [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
methylInheritance/json (API)

# Install 'methylInheritance' in R:

install.packages('methylInheritance', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/adeschen/methylinheritance/issues

Datasets:

demoForTransgenerationalAnalysis - The methylation information from samples over three generations. Information for each generation is stored in a 'methylRawList' format (for demo purpose).
methylInheritanceResults - All observed and permutation results formatted in a 'methylInheritanceResults' class (for demo purpose).
samplesForTransgenerationalAnalysis - All samples information, formated by 'methylKit', in a 'methylRawList' format (for demo purpose).

On BioConductor:methylInheritance-1.37.0(bioc 3.24)methylInheritance-1.36.0(bioc 3.23)

biologicalquestion epigenetics dnamethylation differentialmethylation methylseq software immunooncology statisticalmethod wholegenome sequencing analysis bioconductor bioinformatics cpg differentially-methylated-elements inheritance monte-carlo-sampling permutation

3.70 score 3 scripts 597 downloads 9 exports 90 dependencies

Last updated from:a2ea86b980. Checks:1 WARNING, 8 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	210
linux-devel	ERROR	404
source / vignettes	ERROR	318
linux-release	ERROR	326
macos-release	ERROR	183
macos-oldrel	ERROR	201
windows-devel	ERROR	238
windows-release	ERROR	221
windows-oldrel	ERROR	230
wasm-release	OK	165

Exports:calculateSignificantLevel extractInfo loadAllRDSResults loadConvergenceData mergePermutationAndObservation plotConvergenceGraph plotGraph runObservation runPermutation

Dependencies:askpass bbmle bdsmatrix BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops cigarillo cli coda codetools cpp11 crayon curl data.table emdbook farver fastseg formatR futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 glue gridExtra gtable gtools httr IRanges isoband jsonlite KernSmooth labeling lambda.r lattice lifecycle limma magrittr MASS Matrix mclust methylKit mgcv mime mvtnorm nlme numDeriv openssl plyr qvalue R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RCurl rebus rebus.base rebus.datetimes rebus.numbers rebus.unicode reshape2 restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Vectors S7 scales Seqinfo snow statmod stringi stringr sys vctrs viridisLite withr XML XVector yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate significant level for hypo and hyper conserved elements	calculateSignificantLevel
The methylation information from samples over three generations. Information for each generation is stored in a 'methylRawList' format (for demo purpose).	demoForTransgenerationalAnalysis
Extract the information specific to a subsection of the permutation analysis	extractInfo
Load all RDS files created by the permutation and observation analysis	loadAllRDSResults
Load convergence information from RDS files	loadConvergenceData
Merge the permutation results with the observation results.	mergePermutationAndObservation
All observed and permutation results formatted in a 'methylInheritanceResults' class (for demo purpose).	methylInheritanceResults
Generate a graph showing the convergence for a permutation analysis	plotConvergenceGraph
Generate a graph for a permutation analysis	plotGraph
Print a 'methylInheritanceAllResults' object	print.methylInheritanceAllResults
Run a differential methylation analysis on multi-generational dataset	runObservation
Run all permutations on the specified multi-generational dataset	runPermutation
All samples information, formated by 'methylKit', in a 'methylRawList' format (for demo purpose).	samplesForTransgenerationalAnalysis